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chore: add contributor
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luciorq committed Nov 8, 2024
1 parent cbf6de2 commit 022a2af
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2 changes: 2 additions & 0 deletions .Rbuildignore
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Expand Up @@ -17,3 +17,5 @@
^justfile$
^data-raw$
^vignettes/*_files$
^README\.Rmd$
^README\.html$
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -6,3 +6,4 @@
renv
renv.lock
.Rprofile
README.html
9 changes: 7 additions & 2 deletions DESCRIPTION
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Expand Up @@ -4,8 +4,13 @@ Version: 0.0.6.9007
Authors@R: c(
person("Lucio", "Queiroz", , "luciorqueiroz@gmail.com",
role = c("aut", "cre", "cph"),
comment = c(ORCID = "0000-0002-6090-1834"))
)
comment = c(ORCID = "0000-0002-6090-1834")),
person(given = "Claudio",
family = "Zanettini",
role = c("aut", "ctb"),
email = "claudio.zanettini@gmail.com",
comment = c(ORCID = "0000-0001-5043-8033")
))
Description: Simplifies the execution of command line tools within isolated and
reproducible environments.
It enables users to effortlessly manage Conda environments,
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4 changes: 2 additions & 2 deletions README.Rmd
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Expand Up @@ -123,7 +123,7 @@ rm(temp_out_dir_2)


```{r}
condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env")
condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env", verbose = "output")
```

Then we run the command inside the environment just created which contains a version 0.12.1 of `fastqc`.
Expand Down Expand Up @@ -163,7 +163,7 @@ libcurlVersion()
However, we can choose to use a different version of `curl` run in a different environment. Here, for example, we are installing a different version of `curl` in a separate environment, and checking the version of the newly installed `curl`.

```{r}
condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env")
condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env", verbose = "output")
out <- condathis::run("curl", "--version",
env_name = "curl_env" # environment
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10 changes: 6 additions & 4 deletions README.md
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Expand Up @@ -116,7 +116,8 @@ manages all the library dependencies of `fastqc`, making sure that they
are compatible with the specific operating system.

``` r
condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env")
condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env", verbose = "output")
#> ! Environment fastqc_env already exists.
```

Then we run the command inside the environment just created which
Expand All @@ -143,8 +144,8 @@ In the our temp dir, `fastqc`generated the output files as expected.

``` r
fs::dir_ls(temp_out_dir_2)
#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/Rtmpn2TjYr/sample1_L001_R1_001_fastqc.html
#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/Rtmpn2TjYr/sample1_L001_R1_001_fastqc.zip
#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/RtmpptzAZk/sample1_L001_R1_001_fastqc.html
#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/RtmpptzAZk/sample1_L001_R1_001_fastqc.zip
```

The code that we created with `{condathis}` **uses a system CLI tool but
Expand Down Expand Up @@ -180,7 +181,8 @@ version of `curl` in a separate environment, and checking the version of
the newly installed `curl`.

``` r
condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env")
condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env", verbose = "output")
#> ! Environment curl_env already exists.

out <- condathis::run("curl", "--version",
env_name = "curl_env" # environment
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2 changes: 1 addition & 1 deletion justfile
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Expand Up @@ -13,7 +13,7 @@ github_org := 'luciorq'
\builtin set -euxo pipefail;
R -q -e 'devtools::load_all();styler::style_pkg();';
R -q -e 'devtools::load_all();devtools::document();';
R -q -e 'rmarkdown::render("README.Rmd", encoding = "UTF-8")';
R -q -e 'devtools::load_all();rmarkdown::render("README.Rmd", encoding = "UTF-8")';
R -q -e 'devtools::load_all();devtools::test();';

@check:
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5 changes: 5 additions & 0 deletions man/condathis-package.Rd

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